LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -42.220601 0.0000000) to (14.927237 42.220601 5.1200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1465093 6.2089120 5.1200000 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.220601 0.0000000) to (14.927237 42.220601 5.1200000) create_atoms CPU = 0.003 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1465093 6.2089120 5.1200000 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.220601 0.0000000) to (14.927237 42.220601 5.1200000) create_atoms CPU = 0.003 seconds 274 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 5 29 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 544 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_390178379548_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1743.9317 0 -1743.9317 65576.719 49 0 -1919.9709 0 -1919.9709 5469.2453 Loop time of 1.96523 on 1 procs for 49 steps with 544 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1743.93168592791 -1919.96917101174 -1919.97088385101 Force two-norm initial, final = 234.67540 0.12768102 Force max component initial, final = 70.517285 0.028638066 Final line search alpha, max atom move = 1.0000000 0.028638066 Iterations, force evaluations = 49 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9341 | 1.9341 | 1.9341 | 0.0 | 98.42 Neigh | 0.015434 | 0.015434 | 0.015434 | 0.0 | 0.79 Comm | 0.007908 | 0.007908 | 0.007908 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007798 | | | 0.40 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3355.00 ave 3355 max 3355 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42052.0 ave 42052 max 42052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42052 Ave neighs/atom = 77.301471 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -1919.9709 0 -1919.9709 5469.2453 6453.6259 53 0 -1920.0313 0 -1920.0313 170.77391 6477.4637 Loop time of 0.158334 on 1 procs for 4 steps with 544 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1919.97088385101 -1920.03061635472 -1920.03129632831 Force two-norm initial, final = 41.053320 1.7187033 Force max component initial, final = 34.128242 1.5240025 Final line search alpha, max atom move = 0.00027645047 0.00042131120 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15572 | 0.15572 | 0.15572 | 0.0 | 98.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050147 | 0.00050147 | 0.00050147 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002115 | | | 1.34 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3341.00 ave 3341 max 3341 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42024.0 ave 42024 max 42024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42024 Ave neighs/atom = 77.250000 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.632 | 4.632 | 4.632 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1920.0313 0 -1920.0313 170.77391 Loop time of 3.8208e-05 on 1 procs for 0 steps with 544 atoms 112.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 3.821e-05 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3341.00 ave 3341 max 3341 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42016.0 ave 42016 max 42016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42016 Ave neighs/atom = 77.235294 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.632 | 4.632 | 4.632 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -1920.0313 -1920.0313 14.938439 84.69759 5.1195138 170.77391 170.77391 186.19143 378.10088 -51.970587 2.414897 282.19494 Loop time of 7.728e-06 on 1 procs for 0 steps with 544 atoms 232.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 7.728e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3341.00 ave 3341 max 3341 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21008.0 ave 21008 max 21008 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42016.0 ave 42016 max 42016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42016 Ave neighs/atom = 77.235294 Neighbor list builds = 0 Dangerous builds = 0 544 -1920.03129632831 eV 2.41489697960879 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02